Trinity wrapper not working on local installation
Hello, I am trying to get the trinity wrapper to work on our local galaxy installation using the latest trinity version. The main issue is that the Trinity.pl call has --SS_lib_type None in the script file. The data I am using is unstranded paired end reads and I am selecting None in the tool parameters. I looked at the trinity_all.xml file and it seems like the following code is not working: #if $inputs.library_type != 'None': --SS_lib_type $inputs.library_type #end if I am new to cheeta and python and I am not sure why this code is not working. Any suggestion on how to go about debugging it? Thanks, -Raj
On Thu, Mar 28, 2013 at 4:36 AM, Raj Ayyampalayam <raj76@uga.edu> wrote:
Hello,
I am trying to get the trinity wrapper to work on our local galaxy installation using the latest trinity version.
The main issue is that the Trinity.pl call has --SS_lib_type None in the script file. The data I am using is unstranded paired end reads and I am selecting None in the tool parameters. I looked at the trinity_all.xml file and it seems like the following code is not working:
#if $inputs.library_type != 'None': --SS_lib_type $inputs.library_type #end if
I am new to cheeta and python and I am not sure why this code is not working. Any suggestion on how to go about debugging it?
This is almost certainly a type comparison error, obscured by the cheetah template language and the parameter proxy classes. In Python there is a special object None, which is probably what the library type is using. I would try making this an explicit comparison of strings (a pattern used in many other wrappers, e.g. tools/gatk/*.xml): #if str($inputs.library_type) != 'None': --SS_lib_type $inputs.library_type #end if Or, this might work too: #if $inputs.library_type != None: --SS_lib_type $inputs.library_type #end if (This does seem to be a bug in the trinity wrapper) Peter
I haven't looked at this directly, but it should be using None, in which case the correct comparison is "library_type is None" and "library_type is not None". -- James Taylor, Assistant Professor, Biology/CS, Emory University On Thu, Mar 28, 2013 at 6:35 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Mar 28, 2013 at 4:36 AM, Raj Ayyampalayam <raj76@uga.edu> wrote:
Hello,
I am trying to get the trinity wrapper to work on our local galaxy installation using the latest trinity version.
The main issue is that the Trinity.pl call has --SS_lib_type None in the script file. The data I am using is unstranded paired end reads and I am selecting None in the tool parameters. I looked at the trinity_all.xml file and it seems like the following code is not working:
#if $inputs.library_type != 'None': --SS_lib_type $inputs.library_type #end if
I am new to cheeta and python and I am not sure why this code is not working. Any suggestion on how to go about debugging it?
This is almost certainly a type comparison error, obscured by the cheetah template language and the parameter proxy classes. In Python there is a special object None, which is probably what the library type is using. I would try making this an explicit comparison of strings (a pattern used in many other wrappers, e.g. tools/gatk/*.xml):
#if str($inputs.library_type) != 'None': --SS_lib_type $inputs.library_type #end if
Or, this might work too:
#if $inputs.library_type != None: --SS_lib_type $inputs.library_type #end if
(This does seem to be a bug in the trinity wrapper)
Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
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Hi, None of the solutions that were mentioned fixed the issue. I will do some more debugging later this evening. Thanks, Raj On Thursday, March 28, 2013 12:26:56 PM, James Taylor wrote:
I haven't looked at this directly, but it should be using None, in which case the correct comparison is "library_type is None" and "library_type is not None".
-- James Taylor, Assistant Professor, Biology/CS, Emory University
On Thu, Mar 28, 2013 at 6:35 AM, Peter Cock <p.j.a.cock@googlemail.com> wrote:
On Thu, Mar 28, 2013 at 4:36 AM, Raj Ayyampalayam <raj76@uga.edu> wrote:
Hello,
I am trying to get the trinity wrapper to work on our local galaxy installation using the latest trinity version.
The main issue is that the Trinity.pl call has --SS_lib_type None in the script file. The data I am using is unstranded paired end reads and I am selecting None in the tool parameters. I looked at the trinity_all.xml file and it seems like the following code is not working:
#if $inputs.library_type != 'None': --SS_lib_type $inputs.library_type #end if
I am new to cheeta and python and I am not sure why this code is not working. Any suggestion on how to go about debugging it?
This is almost certainly a type comparison error, obscured by the cheetah template language and the parameter proxy classes. In Python there is a special object None, which is probably what the library type is using. I would try making this an explicit comparison of strings (a pattern used in many other wrappers, e.g. tools/gatk/*.xml):
#if str($inputs.library_type) != 'None': --SS_lib_type $inputs.library_type #end if
Or, this might work too:
#if $inputs.library_type != None: --SS_lib_type $inputs.library_type #end if
(This does seem to be a bug in the trinity wrapper)
Peter ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: http://lists.bx.psu.edu/
To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
-- Bio-informatics consultant QBCG (http://qbcg.uga.edu) 706-542-6092 706-583-0442
participants (3)
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James Taylor -
Peter Cock -
Raj Ayyampalayam